sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4qpp | SAH | Protein arginine N-methyltransferase 6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 1.000 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.637 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.583 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.575 | |
| 4m37 | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.504 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.500 | |
| 1sus | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.497 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.495 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.475 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.475 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.474 | |
| 3cbg | SAH | O-methyltransferase | / | 0.469 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.467 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.467 | |
| 4l45 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.467 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.465 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.464 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.464 | |
| 4h0n | SAH | Dnmt2 | / | 0.464 | |
| 3zcs | CAW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.463 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.462 | |
| 3tr6 | SAH | O-methyltransferase | / | 0.462 | |
| 3dmg | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.458 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.458 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.456 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.456 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.455 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.454 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.454 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 5d7q | AR6 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.451 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.451 | |
| 2dq7 | STU | Tyrosine-protein kinase Fyn | 2.7.10.2 | 0.450 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.450 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.450 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.450 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.450 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.450 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.448 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.448 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.447 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.447 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.446 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.446 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 3b89 | 5GP | 16S rRNA methylase | / | 0.446 | |
| 4cdm | FAD | Deoxyribodipyrimidine photolyase | / | 0.446 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.446 | |
| 5eku | SAH | Arginine N-methyltransferase, putative | / | 0.446 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.445 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.445 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.445 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.445 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.445 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.444 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.444 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.444 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.443 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.443 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.442 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.442 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.440 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3t11 | 3T1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3v9y | 24L | Peroxisome proliferator-activated receptor gamma | / | 0.440 |